Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification and characterization of regenerative innate lymphoid cells from pluripotent stem cells [WT_ILC/R9_iILC_SmartSeq2]

ABSTRACT: We identified that synergistic and inducible expression of Runx1 and Hoxa9 in pluripotent stem cells gave rise to engraftable iHPC capable of developing into mature ILCs in the Rag2-/-Il2rg-/- recipients. We performed single-cell RNA-seq on the entire regenerative CD45.2+GFP+Lin-CD127+ R9-ILC population from the intestine of Rag2-/-Il2rg-/- recipient mice and the CD45.2+Lin-CD127+ WT-ILC population from the intestine of wild type mice (C57BL/6, CD45.2). Single-cell transcriptome illustrated the transcriptome landscape of the R9-ILCs and wild type ILCs including ILC1, ILC2 and ILC3.

ORGANISM(S): Mus musculus

PROVIDER: GSE186777 | GEO | 2022/09/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Identification and characterization of regenerative innate lymphoid cells from pluripotent stem cells [R9_DAY7.5_10X_genomics]

Project description:We identified that synergistic and inducible expression of Runx1 and Hoxa9 in pluripotent stem cells gave rise to engraftable iHPC capable of developing into mature ILCs in the Rag2-/-Il2rg-/- recipients. The regenerative ILCs were detected in multiple tissues including intestine, lung, liver, spleen and thymus. We performed single cell RNA-seq on the sorted GFP+CD45.2+Lin- cells from the bone marrow of recipients at day 7.5 after iHPC transplantation. Single-cell transcriptome illustrated the existence of regenerative ILC-related progenitors including iLP, iILCP, iILC1/3P and iILC2P, and the cellular trajectory of regenerative ILCs development in vivo was closely resembles the natural ILCs development.

2022-09-30 | GSE186776 | GEO

Identification and characterization of regenerative innate lymphoid cells from pluripotent stem cells [WT-CHILP/iR9-CHILP_SmartSeq2]

Project description:We identified that synergistic and inducible expression of Runx1 and Hoxa9 in pluripotent stem cells (PSCs) gave rise to engraftable iHPC capable of developing into common helper innate lymphoid progenitors (CHILPs) in the Rag2-/-Il2rg-/- recipients. To assess the gene-expression pattern of the PSC-derived R9-iCHILPs, we performed single-cell RNA-seq on the regenerative CD45.2+GFP+Lin-CD127+CD135-α4β7+Sca1mid/-CD25- R9-iCHILPs from the bone marrow of Rag2-/-Il2rg-/- recipient mice and the CD45.2+Lin-CD127+CD135-α4β7+Sca1mid/-CD25- WT-CHILPs from the bone marrow of wild type mice (C57BL/6, CD45.2).

2022-09-30 | GSE210861 | GEO

Gene expression profiling of murine innate lymphoid cells

Project description:Innate lymphoid cells (ILCs) are a recently recognized heterogenous group of immune cells that are critical in orchestrating immunity and inflammation in the intestine, but whether ILCs influence immune responses or tissue homeostasis at other mucosal sites remains poorly characterized. Here we identify a population of lung-resident ILCs in mice and humans that expressed the alloantigen Thy-1 (CD90), interleukin 2 (IL-2) receptor a-chain (CD25), IL-7 receptor a-chain (CD127) and the IL-33 receptor subunit T1-ST2. Notably, mouse ILCs accumulated in the lung after infection with influenza virus, and depletion of ILCs resulted in loss of airway epithelial integrity, diminished lung function and impaired airway remodeling. These defects were restored by administration of the lung ILC product amphiregulin. Collectively, our results demonstrate a critical role for lung ILCs in restoring airway epithelial integrity and tissue homeostasis after infection with influenza virus. As part of this study, we performed gene expression profiling to examine how the transcriptional signatures compared between murine naïve group 2 lung ILC and group 3 splenic LTi cell populations. Group 2 ILCs from the lung (Lin- CD90+ CD25+ T1/ST2+) and Group 3 LTi cells from the spleen (Lin- CD90+ CD25+ CD4+) were sort-purified from naive wildtype C57BL/6 mice using BD FACS Aria. Four biological replicates were collected, each replicate containing 1.5 x 104 to 2 x104 cells sorted to a purity >97% from six pooled lungs (ILCs) or 10 pooled spleens (LTi cells). Cells were sorted directly into TRIzol LS (Invitrogen), then mRNA was isolated, amplified, labeled, and hybridized to Affymetrix GeneChip (Mouse Gene 1.0 ST).

2013-04-30 | E-GEOD-46468 | biostudies-arrayexpress

Expression data from small intestinal Lin-c-Kit+Sca-1- cells and Lin-c-Kit-Sca-1- cells.

Project description:Small intestinal innate lymphoid cells (ILCs) are known to regulate intestinal epithelial cell homeostasis and to help prevent pathogenic bacterial infections, by producing IL-22. However, other functions of these cells and the lineal relationship between ILCs and lymphoid or myeloid cells have not been clear. We performed a global gene expression analysis to examine which genes are highly expressed by small intestinal ILCs (Lin-c-Kit+Sca-1- cells) compared with non-ILCs (Lin-c-Kit-Sca-1- cells). To examine the gene expression profiles of ILCs within the small intestinal lamina propria (LP), we isolated Lingeage (Lin)-c-Kit+Sca-1- cells [consisting of NKp46+ ILC22 (Lin-c-Kit+Sca-1-NKp46+ cells) and LTi-like ILC (Lin-c-Kit+Sca-1-CD4+ cells)] as the ILC population, and Lin-c-Kit-Sca-1- cells as the non-ILC population, from the small intestinal LP of 8 week-old mice by FACS, then compared the gene expression profiles between these two populations by microarray analysis.

2012-09-15 | E-GEOD-40882 | biostudies-arrayexpress

Identification of human cytotoxic ILC3s

Project description:Human ILCs are classically categorized into five subsets; cytotoxic CD127-CD94+ NK cells and non-cytotoxic CD127+CD94-, ILC1s, ILC2s, ILC3s and LTi cells. Here, we identify a novel subset within the CD127+ ILC population, characterized by the expression of the cytotoxic marker CD94. These CD94+ ILCs strongly resemble conventional ILC3s in terms of phenotype, transcriptome and cytokine production, but are highly cytotoxic. IL-15 was unable to induce differentiation of CD94+ ILCs towards mature NK cells. Instead, CD94+ ILCs retained RORγt, CD127 and CD200R expression and produced IL-22 in response to IL-15. Culturing non-cytotoxic CD127+ ILC1s or ILC3s with IL-12 induced upregulation of CD94 and cytotoxic activity, effects that were not observed with IL-15 stimulation. Thus, human helper ILCs can acquire a cytotoxic program without differentiating into NK cells.

2020-09-14 | GSE147231 | GEO

Transcriptomic analysis of femoral diaphysis and primary osteoprogenitor cells cultures from mouse strains with SHIP1 deficiency and controls

Project description:Investigation of the SHIP1 (Inpp5d)-dependent and Rag2/Il2rg-dependent transcriptional changes in bone and osteoprogenitor cells cultures from murine strains with SHIP1 deficiency (Inpp5dm1Btlr/ m1Btlr, http://www.informatics.jax.org/allele/key/65037) and controls. Specifically, transcriptomic analysis was performed from femoral diaphysis from SHIPstyx/styx, SHIP1+/styx, wild-type (C57BL6/J), Rag2-/-/Il2rg-/-/SHIP1styx/styx, Rag2-/-/Il2rg-/-/SHIP1+/styx, and Rag2-/-/Il2rg-/-/SHIP1+/+ mice (n=3 for each genotype). Alternatively, osteoprogenitor cells isolated from bone marrow from the same genotypes as above were differentiated in vitro into primary osteoclasts in the presence or absence of RANKL. After 5 days, RNA was extracted from these cultures for transcriptomic analysis (n=3 for each genotype). Experimental Designs: Transcripts were analyzed in femoral diaphysis of SHIPstyx/styx, SHIP1+/styx, wild-type (C57BL6/J), Rag2-/-/Il2rg-/-/SHIP1styx/styx, Rag2-/-/Il2rg-/-/SHIP1+styx, and Rag2-/-/Il2rg-/-/SHIP1+/+ mice (n=3 for each genotype). Alternatively, transcripts were analyzed in primary osteoclast cultures from bone marrow cells isolated from SHIPstyx/styx, SHIP1+/styx, wild-type (C57BL6/J), Rag2-/-/Il2rg-/-/SHIP1styx/styx, Rag2-/-/Il2rg-/-/SHIP1+styx, and Rag2-/-/Il2rg-/-/SHIP1+/+ mice (n=3 for each genotype), which were supplemented or not with RANKL.

2024-02-21 | E-MTAB-13164 | biostudies-arrayexpress

Gene expression profiling of murine innate lymphoid cells

2013-04-30 | GSE46468 | GEO

Identification of aceNKPs, a committed common progenitor of the ILC1 and NK cell continuum

Project description:The development of innate lymphoid cell (ILC) transcription factor reporter mice has shown a previously unexpected complexity in ILC haematopoiesis. Using novel polychromic mice to achieve higher phenotypic resolution we have characterised bone marrow progenitors that are committed to the group 1 ILC lineage. These common ILC1/NK progenitors, which we call ‘aceNKPs’, are defined as lineage–Id2+IL-7Ra+CD25–a4b7–NKG2A/C/E+Bcl11b–. In vitro, aceNKPs differentiate into group 1 ILCs, including NK-like cells that express Eomes without the requirement for IL-15, and produce IFN-g and perforin upon IL-15 stimulation. Following reconstitution of Rag2–/–Il2rg–/– hosts, aceNKPs give rise to a spectrum of mature ILC1/NK cells (regardless of their tissue location) that cannot be clearly segregated into the traditional ILC1 and NK subsets, suggesting that group 1 ILCs constitute a dynamic continuum of ILCs that can develop from a common progenitor. In addition, aceNKP-derived ILC1/NK cells effectively ameliorate tumour burden in a model of lung metastasis where they acquired a cytotoxic NK cell phenotype. Our results identify the primary ILC1/NK progenitor that lacks ILC2 or ILC3 potential and is strictly committed to ILC1/NK cell production irrespective of tissue homing.

2022-11-02 | GSE213814 | GEO

Expression data from long-term Ebf1-deficient, CD19+, Bcl2tg cells

Project description:An assessment of a role of Ebf1 in committed B lineage cells. In this study, we adopted the strategy of deleting Ebf1 after reconstitution of Rag2-/-Il2rg-/- mice and found that committed pre-B cells could be converted into T cells and ILCs upon deletion of Ebf1.

2013-06-01 | GSE46349 | GEO

Myeloid, B, and T lineage regeneration from pluripotent stem cells by defined transcription factors

Project description:We identified that synergistic and inducible expression of specific transcription factors in pluripotent stem cells gave rise to engraftable iHPC capable of developing into multiple lineages including myeloid cells, T cells, and B cells in the C57BL/6 recipients. The regenerative myeloid, T, and B cells were detected in multiple tissues including peripheral blood, bone marrow and spleen. We performed single cell RNA-seq on the sorted GFP+CD45.2+ cells from the peripheral blood of recipients at 16 weeks after iHPC transplantation. Single-cell transcriptome illustrated the existence of regenerative myeloid cells, T cells, and B cells. The cell hierarchy of regenerative myeloid cells, T cells, and B cells in vivo resembles those of natural counterparts.

2022-11-24 | GSE189736 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data